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(-) Description

Title :  CRYSTAL STRUCTURE OF ORGANOPHOSPHORUS HYDROLASE FROM GEOBACILLUS STEAROTHERMOPHILUS STRAIN 10, WITH GLYCEROL BOUND
 
Authors :  R. Hawwa, J. Aikens, R. J. Turner, B. Santarsiero, A. Mesecar
Date :  31 Oct 08  (Deposition) - 15 Sep 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.07
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Alpha-Beta Barrel, Amidohydrolase, Binuclear Metal Enzyme, Glycerol- Bound, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Hawwa, J. Aikens, R. J. Turner, B. D. Santarsiero, A. D. Mesecar
Structural Basis For Thermostability Revealed Through The Identification And Characterization Of A Highly Thermostabl Phosphotriesterase-Like Lactonase From Geobacillus Stearothermophilus.
Arch. Biochem. Biophys. V. 488 109 2009
PubMed-ID: 19615330  |  Reference-DOI: 10.1016/J.ABB.2009.06.005

(-) Compounds

Molecule 1 - ORGANOPHOSPHORUS HYDROLASE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: GEOBACILLUS STEAROTHERMOPHILUS
    Organism Taxid: 272567
    Strain: 10

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 8)

Asymmetric/Biological Unit (3, 8)
No.NameCountTypeFull Name
1CO4Ligand/IonCOBALT (II) ION
2GOL2Ligand/IonGLYCEROL
3KCX2Mod. Amino AcidLYSINE NZ-CARBOXYLIC ACID

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH B:25 , HIS B:123 , PHE B:126 , TYR B:128 , TYR B:197 , KCX B:243 , ARG B:328 , ASP B:364 , CO B:501 , HOH B:584 , HOH B:629BINDING SITE FOR RESIDUE GOL B 601
2AC2SOFTWAREHOH A:20 , TYR A:197 , KCX A:243 , HIS A:276 , HIS A:304 , CO A:501 , GOL A:601BINDING SITE FOR RESIDUE CO A 502
3AC3SOFTWAREHOH A:20 , HIS A:123 , TYR A:128 , TYR A:197 , ARG A:328 , ASP A:364 , CO A:501 , CO A:502 , HOH A:568BINDING SITE FOR RESIDUE GOL A 601
4AC4SOFTWAREHOH A:20 , HIS A:121 , HIS A:123 , KCX A:243 , ASP A:364 , CO A:502 , GOL A:601BINDING SITE FOR RESIDUE CO A 501
5AC5SOFTWAREHOH B:25 , HIS B:121 , HIS B:123 , KCX B:243 , ASP B:364 , GOL B:601BINDING SITE FOR RESIDUE CO B 501
6AC6SOFTWAREHOH B:25 , TYR B:197 , KCX B:243 , HIS B:276 , HIS B:304BINDING SITE FOR RESIDUE CO B 502

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3F4C)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3F4C)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3F4C)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3F4C)

(-) Exons   (0, 0)

(no "Exon" information available for 3F4C)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:324
 aligned with D0VX06_GEOSE | D0VX06 from UniProtKB/TrEMBL  Length:332

    Alignment length:324
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322    
         D0VX06_GEOSE     3 KTVETVLGPVPVEQLGKTLIHEHFLFGYPGFQGDVTRGTFREDEALRVAVEAAEKMKRHGIQTVVDPTPNDCGRNPAFLRRVAEETGLNIICATGYYYEGEGAPPYFQFRRLLGTAEDDIYDMFMAELTEGIADTGIKAGVIKLASSKGRITEYEKMFFRAAARAQKETGAVIITHTQEGTMGPEQAAYLLEHGADPKKIVIGHMCGNTDPDYHRKTLAYGVYIAFDRFGIQGMVGAPTDEERVRTLLALLRDGYEKQIMLSHDTVNVWLGRPFTLPEPFAEMMKNWHVEHLFVNIIPALKNEGIRDEVLEQMFIGNPAALFSA 326
               SCOP domains d3f4ca_ A: automated matches                                                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeee..eeee.hhh..ee...eeee...hhhhhh.....hhhhhhhhhhhhhhhhhh....eeee..hhhhh.hhhhhhhhhhhhh.eeeeee.........hhhhhhhhhh.hhhhhhhhhhhhhhhh..........eeeee......hhhhhhhhhhhhhhhhhhh.eeeee.....hhhhhhhhhhhh..hhh.eee.hhhhh.hhhhhhhhhh...eeee............hhhhhhhhhhhhhhh.hhh.eee....eeee.......hhhhhhhh.....hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3f4c A 101 KTVETVLGPVPVEQLGKTLIHEHFLFGYPGFQGDVTRGTFREDEALRVAVEAAEKMKRHGIQTVVDPTPNDCGRNPAFLRRVAEETGLNIICATGYYYEGEGAPPYFQFRRLLGTAEDDIYDMFMAELTEGIADTGIKAGVIkLASSKGRITEYEKMFFRAAARAQKETGAVIITHTQEGTMGPEQAAYLLEHGADPKKIVIGHMCGNTDPDYHRKTLAYGVYIAFDRFGIQGMVGAPTDEERVRTLLALLRDGYEKQIMLSHDTVNVWLGRPFTLPEPFAEMMKNWHVEHLFVNIIPALKNEGIRDEVLEQMFIGNPAALFSA 424
                                   110       120       130       140       150       160       170       180       190       200       210       220       230       240  |    250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420    
                                                                                                                                                                        243-KCX                                                                                                                                                                                 


Chain B from PDB  Type:PROTEIN  Length:324
 aligned with D0VX06_GEOSE | D0VX06 from UniProtKB/TrEMBL  Length:332

    Alignment length:324
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322    
         D0VX06_GEOSE     3 KTVETVLGPVPVEQLGKTLIHEHFLFGYPGFQGDVTRGTFREDEALRVAVEAAEKMKRHGIQTVVDPTPNDCGRNPAFLRRVAEETGLNIICATGYYYEGEGAPPYFQFRRLLGTAEDDIYDMFMAELTEGIADTGIKAGVIKLASSKGRITEYEKMFFRAAARAQKETGAVIITHTQEGTMGPEQAAYLLEHGADPKKIVIGHMCGNTDPDYHRKTLAYGVYIAFDRFGIQGMVGAPTDEERVRTLLALLRDGYEKQIMLSHDTVNVWLGRPFTLPEPFAEMMKNWHVEHLFVNIIPALKNEGIRDEVLEQMFIGNPAALFSA 326
               SCOP domains d3f4cb_ B: automated matches                                                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeee..eeee.hhh..ee...eeee...hhhhhh.....hhhhhhhhhhhhhhhhhh....eeee........hhhhhhhhhhhhh.eeeeee...hhhhh.hhhhhhhhhh.hhhhhhhhhhhhhhhh..........eeeee......hhhhhhhhhhhhhhhhhhh.eeeee.....hhhhhhhhhhhh..hhh.eee.hhhhh.hhhhhhhhhh...eeee............hhhhhhhhhhhhhhh.hhh.eee....eeee.......hhhhhhhh.....hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3f4c B 101 KTVETVLGPVPVEQLGKTLIHEHFLFGYPGFQGDVTRGTFREDEALRVAVEAAEKMKRHGIQTVVDPTPNDCGRNPAFLRRVAEETGLNIICATGYYYEGEGAPPYFQFRRLLGTAEDDIYDMFMAELTEGIADTGIKAGVIkLASSKGRITEYEKMFFRAAARAQKETGAVIITHTQEGTMGPEQAAYLLEHGADPKKIVIGHMCGNTDPDYHRKTLAYGVYIAFDRFGIQGMVGAPTDEERVRTLLALLRDGYEKQIMLSHDTVNVWLGRPFTLPEPFAEMMKNWHVEHLFVNIIPALKNEGIRDEVLEQMFIGNPAALFSA 424
                                   110       120       130       140       150       160       170       180       190       200       210       220       230       240  |    250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420    
                                                                                                                                                                        243-KCX
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3F4C)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3F4C)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (D0VX06_GEOSE | D0VX06)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0009056    catabolic process    The chemical reactions and pathways resulting in the breakdown of substances, including the breakdown of carbon compounds with the liberation of energy for use by the cell or organism.

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 Related Entries

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        D0VX06_GEOSE | D0VX06: 3f4d

(-) Related Entries Specified in the PDB File

3f4d CRYSTAL STRUCTURE OF ORGANOPHOSPHORUS HYDROLASE FROM GEOBACILLUS STEAROTHERMOPHILUS STRAIN 10